How to stop colours of overlapping spheres from mixing?
Try changing the &quot;color&quot; line to:
colors = { 'In' : (0.0, 0.0, 255.0, 1.0), 'Ga' : (255.0, 0.4, 0.4, 1.0), 'bond': (0.05, 0.05, 0.05 , 1.0) }